data_36022 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of two TTTA repeats ; _BMRB_accession_number 36022 _BMRB_flat_file_name bmr36022.str _Entry_type original _Submission_date 2016-09-13 _Accession_date 2016-10-31 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Guo Pei . . 2 Lam 'Sik Lok' L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 90 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-11-03 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 36020 'Structure of two CCTG repeats' stop_ _Original_release_date 2016-11-03 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Minidumbbell: A New Form of Native DNA Structure ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27589409 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Guo Pei . . 2 Lam 'Sik Lok' L. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the Americal Chemical Society' _Journal_volume 138 _Journal_issue . _Journal_ASTM JACSAT _Journal_ISSN 1520-5126 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 12534 _Page_last 12540 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_NA $entity_NA entity_NA $entity_NA entity_NA $entity_NA entity_NA $entity_NA entity_NA $entity_NA entity_NA $entity_NA entity_NA $entity_NA stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common "DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3')" _Molecular_mass 2406.613 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; TTTATTTA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DT 3 3 DT 4 4 DA 5 5 DT 6 6 DT 7 7 DT 8 8 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_NA _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'SODIUM ION' _BMRB_code NA _PDB_code NA _Molecular_mass 22.990 _Mol_charge 1 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons NA NA NA . 1 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 'Staphylococcus aureus' 1280 Bacteria . Staphylococcus . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details "1.0 mM DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3'), 10 mM sodium phosphate, 0.1 mM DSS, 100% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mM 'natural abundance' DSS 0.1 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' D2O 100 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 700 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceII _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 7.0 . pH pressure 1 . atm temperature 278 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'Non-labile and labile proton chemical shifts were measured at 278 and 273 K, respectively.' loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 DT H1' H 6.15 0.01 1 2 1 1 DT H2' H 2.02 0.01 . 3 1 1 DT H2'' H 2.35 0.01 . 4 1 1 DT H3 H 13.5 0.02 1 5 1 1 DT H3' H 4.85 0.01 1 6 1 1 DT H4' H 4.36 0.01 1 7 1 1 DT H5' H 3.88 0.01 . 8 1 1 DT H5'' H 3.88 0.01 . 9 1 1 DT H6 H 7.49 0.01 1 10 1 1 DT H71 H 1.49 0.01 1 11 1 1 DT H72 H 1.49 0.01 1 12 1 1 DT H73 H 1.49 0.01 1 13 2 2 DT H1' H 6.37 0.01 1 14 2 2 DT H2' H 2.05 0.01 . 15 2 2 DT H2'' H 2.41 0.01 . 16 2 2 DT H3 H 11.1 0.02 1 17 2 2 DT H3' H 4.85 0.01 1 18 2 2 DT H4' H 4.43 0.01 1 19 2 2 DT H5' H 4.11 0.01 . 20 2 2 DT H5'' H 4.28 0.01 . 21 2 2 DT H6 H 7.90 0.01 1 22 2 2 DT H71 H 2.06 0.01 1 23 2 2 DT H72 H 2.06 0.01 1 24 2 2 DT H73 H 2.06 0.01 1 25 3 3 DT H1' H 5.24 0.01 1 26 3 3 DT H2' H 1.71 0.01 . 27 3 3 DT H2'' H 2.03 0.01 . 28 3 3 DT H3 H 11.0 0.02 1 29 3 3 DT H3' H 4.60 0.01 1 30 3 3 DT H4' H 3.92 0.01 1 31 3 3 DT H5' H 3.92 0.01 . 32 3 3 DT H5'' H 3.92 0.01 . 33 3 3 DT H6 H 7.45 0.01 1 34 3 3 DT H71 H 1.41 0.01 1 35 3 3 DT H72 H 1.41 0.01 1 36 3 3 DT H73 H 1.41 0.01 1 37 4 4 DA H1' H 6.47 0.01 1 38 4 4 DA H2 H 8.15 0.01 1 39 4 4 DA H2' H 3.15 0.01 . 40 4 4 DA H2'' H 3.15 0.01 . 41 4 4 DA H3' H 4.96 0.01 1 42 4 4 DA H4' H 4.47 0.01 1 43 4 4 DA H5' H 4.06 0.01 . 44 4 4 DA H5'' H 4.06 0.01 . 45 4 4 DA H8 H 8.35 0.01 1 46 5 5 DT H1' H 6.30 0.01 1 47 5 5 DT H2' H 2.14 0.01 . 48 5 5 DT H2'' H 2.47 0.01 . 49 5 5 DT H3 H 13.5 0.02 1 50 5 5 DT H3' H 4.82 0.01 1 51 5 5 DT H4' H 4.47 0.01 1 52 5 5 DT H5' H 4.10 0.01 . 53 5 5 DT H5'' H 4.38 0.01 . 54 5 5 DT H6 H 7.42 0.01 1 55 5 5 DT H71 H 1.36 0.01 1 56 5 5 DT H72 H 1.36 0.01 1 57 5 5 DT H73 H 1.36 0.01 1 58 6 6 DT H1' H 6.40 0.01 1 59 6 6 DT H2' H 2.24 0.01 . 60 6 6 DT H2'' H 2.61 0.01 . 61 6 6 DT H3 H 11.1 0.02 1 62 6 6 DT H3' H 4.81 0.01 1 63 6 6 DT H4' H 4.38 0.01 1 64 6 6 DT H5' H 4.13 0.01 . 65 6 6 DT H5'' H 4.21 0.01 . 66 6 6 DT H6 H 7.81 0.01 1 67 6 6 DT H71 H 2.00 0.01 1 68 6 6 DT H72 H 2.00 0.01 1 69 6 6 DT H73 H 2.00 0.01 1 70 7 7 DT H1' H 5.59 0.01 1 71 7 7 DT H2' H 1.78 0.01 . 72 7 7 DT H2'' H 2.06 0.01 . 73 7 7 DT H3 H 11.0 0.02 1 74 7 7 DT H3' H 4.61 0.01 1 75 7 7 DT H4' H 3.94 0.01 1 76 7 7 DT H5' H 3.94 0.01 . 77 7 7 DT H5'' H 3.94 0.01 . 78 7 7 DT H6 H 7.57 0.01 1 79 7 7 DT H71 H 1.55 0.01 1 80 7 7 DT H72 H 1.55 0.01 1 81 7 7 DT H73 H 1.55 0.01 1 82 8 8 DA H1' H 6.28 0.01 1 83 8 8 DA H2 H 8.17 0.01 1 84 8 8 DA H2' H 3.07 0.01 . 85 8 8 DA H2'' H 2.73 0.01 . 86 8 8 DA H3' H 4.86 0.01 1 87 8 8 DA H4' H 4.16 0.01 1 88 8 8 DA H5' H 3.80 0.01 . 89 8 8 DA H5'' H 3.98 0.01 . 90 8 8 DA H8 H 8.23 0.01 1 stop_ save_